{"seq": 1, "t": "2026-08-27T21:50:13-04:00", "type": "meta", "trace_version": 1, "scenario": "01-happy-path", "title": "Register FASTQs and walk to samplesheets", "gars_version": "0.9.2", "gars_commit": "953184da89258cdabdd89e8ff04e02469fd792b9", "model": "claude-fable-5", "recorded_at": "2026-08-27T21:50:13-04:00", "honesty": {"real": ["The stage contracts, helper scripts, exit codes and refusal templates are the real GARS v0.9.2, unmodified.", "The agent is a real Claude agent executing the contracts; every message shown was actually produced by it.", "Every filesystem snapshot was walked from disk immediately after the step it follows."], "miniaturized": ["The sequencing run is synthetic: 4 samples, paired-end, a few kilobytes each — real cohorts are terabytes.", "This scenario stops where HPC begins; pipeline stages (nf-core, SLURM) are precomputed in other scenarios."], "instrumentation": ["The agent invoked each helper through a recording wrapper that preserves stdout and exit codes verbatim.", "The user side of the dialogue was driven by the recording harness; the human design-gate edit was made by it as the user.", "Claude Code's workspace hook layer was not armed in the recording session; helper-level refusals were live."]}}
{"seq": 2, "t": "2026-08-27T21:50:13-04:00", "type": "snapshot", "label": "the sequencing run as delivered", "root_label": "seqrun", "files": [{"path": "M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "f74c95074243940580d47cc245633ffe75c1423b30bf8d9370be49681eb0f77c"}, {"path": "M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "7fded24a22de82ffb1b672a3182c7adcfb3abf3db1a8b3d72c75492e45aa4ee8"}, {"path": "M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "b5f6452fa052bb84cad34fc1750153e33f93767c68c93308cfae1edb38c95213"}, {"path": "M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "cb4d9ccb88ca34020c8e014be7cb7a21b6ee74fb9ca6ed448557609561b7f212"}, {"path": "M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "ecc0a2314f582f0fe83aefd217671d6a1582a70e4f78e461df632278fa2b4a83"}, {"path": "M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "bf267f019e7d73ef684c83f0d0a1d333002b8b452e513d74495234cd40e10cca"}, {"path": "M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "7e029513e5466d9af80aa369aa1cd5a1a49c913a06b01a9f8e6c6a5110964dd0"}, {"path": "M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "file", "mode": "0644", "size": 90, "sha256": "d63c170ddc934cfe7759e0aed21a02d64aacdb876b3518fda83e6692a5db01b1"}, {"path": "notes.txt", "kind": "file", "mode": "0644", "size": 82, "content": "Run notes from the sequencing core - not a FASTQ; stage 00 must ignore this file.\n"}]}
{"seq": 3, "t": "2026-08-27T21:50:13-04:00", "type": "user", "text": "Start a new project called Macrophage Polarization, bulk RNA-seq. The data is in /private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage."}
{"seq": 4, "t": "2026-08-27T21:51:50-04:00", "type": "command", "argv": ["bash", "_system/session_state.sh"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "# Project state — derived from the filesystem, authority: STATUS + HISTORY.md\n(template v0.9.2 · generated by _system/project_state.py; a render, not a record)\n\n(no projects yet)\n", "stdout_json": null, "stderr": "", "stage": "00_initialize_project", "step": "session_state.sh (session boot)"}
{"seq": 5, "t": "2026-08-27T21:52:03-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "assays"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assays\": [\n    {\n      \"assay\": \"ATAC-seq (bulk)\",\n      \"assay_id\": \"atacseq_bulk\",\n      \"n\": \"01\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-atacseq-wrapper\",\n          \"substage\": \"01_nfcore-atacseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"ChIP-seq (bulk)\",\n      \"assay_id\": \"chipseq_bulk\",\n      \"n\": \"02\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-chipseq-wrapper\",\n          \"substage\": \"01_nfcore-chipseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"CUT&RUN / CUT&Tag\",\n      \"assay_id\": \"cutandrun\",\n      \"n\": \"03\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-cutandrun-wrapper\",\n          \"substage\": \"01_nfcore-cutandrun-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"Bisulfite (WGBS/RRBS)\",\n      \"assay_id\": \"methylseq\",\n      \"n\": \"04\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-methylseq-wrapper\",\n          \"substage\": \"01_nfcore-methylseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"Bulk RNA-seq\",\n      \"assay_id\": \"rnaseq_bulk\",\n      \"n\": \"05\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-rnaseq-wrapper\",\n          \"substage\": \"01_nfcore-rnaseq-wrapper\"\n        },\n        {\n          \"skill\": \"rnaseq-de\",\n          \"substage\": \"02_rnaseq-de\"\n        }\n      ]\n    }\n  ],\n  \"command\": \"assays\",\n  \"ok\": true\n}\n", "stdout_json": {"assays": [{"assay": "ATAC-seq (bulk)", "assay_id": "atacseq_bulk", "n": "01", "substages": [{"skill": "nfcore-atacseq-wrapper", "substage": "01_nfcore-atacseq-wrapper"}]}, {"assay": "ChIP-seq (bulk)", "assay_id": "chipseq_bulk", "n": "02", "substages": [{"skill": "nfcore-chipseq-wrapper", "substage": "01_nfcore-chipseq-wrapper"}]}, {"assay": "CUT&RUN / CUT&Tag", "assay_id": "cutandrun", "n": "03", "substages": [{"skill": "nfcore-cutandrun-wrapper", "substage": "01_nfcore-cutandrun-wrapper"}]}, {"assay": "Bisulfite (WGBS/RRBS)", "assay_id": "methylseq", "n": "04", "substages": [{"skill": "nfcore-methylseq-wrapper", "substage": "01_nfcore-methylseq-wrapper"}]}, {"assay": "Bulk RNA-seq", "assay_id": "rnaseq_bulk", "n": "05", "substages": [{"skill": "nfcore-rnaseq-wrapper", "substage": "01_nfcore-rnaseq-wrapper"}, {"skill": "rnaseq-de", "substage": "02_rnaseq-de"}]}], "command": "assays", "ok": true}, "stderr": "", "stage": "00_initialize_project", "step": "assays (Process step 3)"}
{"seq": 6, "t": "2026-08-27T21:53:30-04:00", "type": "agent", "text": "Project title: Macrophage Polarization -> directory Macrophage_Polarization\n\nSupported assays:\n\n  01  ATAC-seq (bulk)  (atacseq_bulk)\n      pipeline: 01_nfcore-atacseq-wrapper\n      skills:   nfcore-atacseq-wrapper\n\n  02  ChIP-seq (bulk)  (chipseq_bulk)\n      pipeline: 01_nfcore-chipseq-wrapper\n      skills:   nfcore-chipseq-wrapper\n\n  03  CUT&RUN / CUT&Tag  (cutandrun)\n      pipeline: 01_nfcore-cutandrun-wrapper\n      skills:   nfcore-cutandrun-wrapper\n\n  04  Bisulfite (WGBS/RRBS)  (methylseq)\n      pipeline: 01_nfcore-methylseq-wrapper\n      skills:   nfcore-methylseq-wrapper\n\n  05  Bulk RNA-seq  (rnaseq_bulk)\n      pipeline: 01_nfcore-rnaseq-wrapper -> 02_rnaseq-de\n      skills:   nfcore-rnaseq-wrapper, rnaseq-de\n\nYour request matches 05.\n\nReply with a comma-separated list of IDs (e.g. `01` or `01,02`). Assay names work too.", "template": "T3", "stage": "00_initialize_project", "wait_point": true}
{"seq": 7, "t": "2026-08-27T21:53:45-04:00", "type": "user", "text": "05"}
{"seq": 8, "t": "2026-08-27T21:54:27-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "assays", "--select", "05"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assay_ids\": [\n    \"rnaseq_bulk\"\n  ],\n  \"assays\": [\n    {\n      \"assay\": \"ATAC-seq (bulk)\",\n      \"assay_id\": \"atacseq_bulk\",\n      \"n\": \"01\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-atacseq-wrapper\",\n          \"substage\": \"01_nfcore-atacseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"ChIP-seq (bulk)\",\n      \"assay_id\": \"chipseq_bulk\",\n      \"n\": \"02\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-chipseq-wrapper\",\n          \"substage\": \"01_nfcore-chipseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"CUT&RUN / CUT&Tag\",\n      \"assay_id\": \"cutandrun\",\n      \"n\": \"03\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-cutandrun-wrapper\",\n          \"substage\": \"01_nfcore-cutandrun-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"Bisulfite (WGBS/RRBS)\",\n      \"assay_id\": \"methylseq\",\n      \"n\": \"04\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-methylseq-wrapper\",\n          \"substage\": \"01_nfcore-methylseq-wrapper\"\n        }\n      ]\n    },\n    {\n      \"assay\": \"Bulk RNA-seq\",\n      \"assay_id\": \"rnaseq_bulk\",\n      \"n\": \"05\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-rnaseq-wrapper\",\n          \"substage\": \"01_nfcore-rnaseq-wrapper\"\n        },\n        {\n          \"skill\": \"rnaseq-de\",\n          \"substage\": \"02_rnaseq-de\"\n        }\n      ]\n    }\n  ],\n  \"command\": \"assays\",\n  \"invalid\": [],\n  \"ok\": true,\n  \"selected\": [\n    {\n      \"assay\": \"Bulk RNA-seq\",\n      \"assay_id\": \"rnaseq_bulk\",\n      \"n\": \"05\",\n      \"substages\": [\n        {\n          \"skill\": \"nfcore-rnaseq-wrapper\",\n          \"substage\": \"01_nfcore-rnaseq-wrapper\"\n        },\n        {\n          \"skill\": \"rnaseq-de\",\n          \"substage\": \"02_rnaseq-de\"\n        }\n      ]\n    }\n  ]\n}\n", "stdout_json": {"assay_ids": ["rnaseq_bulk"], "assays": [{"assay": "ATAC-seq (bulk)", "assay_id": "atacseq_bulk", "n": "01", "substages": [{"skill": "nfcore-atacseq-wrapper", "substage": "01_nfcore-atacseq-wrapper"}]}, {"assay": "ChIP-seq (bulk)", "assay_id": "chipseq_bulk", "n": "02", "substages": [{"skill": "nfcore-chipseq-wrapper", "substage": "01_nfcore-chipseq-wrapper"}]}, {"assay": "CUT&RUN / CUT&Tag", "assay_id": "cutandrun", "n": "03", "substages": [{"skill": "nfcore-cutandrun-wrapper", "substage": "01_nfcore-cutandrun-wrapper"}]}, {"assay": "Bisulfite (WGBS/RRBS)", "assay_id": "methylseq", "n": "04", "substages": [{"skill": "nfcore-methylseq-wrapper", "substage": "01_nfcore-methylseq-wrapper"}]}, {"assay": "Bulk RNA-seq", "assay_id": "rnaseq_bulk", "n": "05", "substages": [{"skill": "nfcore-rnaseq-wrapper", "substage": "01_nfcore-rnaseq-wrapper"}, {"skill": "rnaseq-de", "substage": "02_rnaseq-de"}]}], "command": "assays", "invalid": [], "ok": true, "selected": [{"assay": "Bulk RNA-seq", "assay_id": "rnaseq_bulk", "n": "05", "substages": [{"skill": "nfcore-rnaseq-wrapper", "substage": "01_nfcore-rnaseq-wrapper"}, {"skill": "rnaseq-de", "substage": "02_rnaseq-de"}]}]}, "stderr": "", "stage": "00_initialize_project", "step": "assays --select (Process step 4)"}
{"seq": 9, "t": "2026-08-27T21:54:33-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "create", "--title", "Macrophage Polarization", "--assays", "rnaseq_bulk"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assays\": [\n    {\n      \"assay_id\": \"rnaseq_bulk\",\n      \"requested\": \"rnaseq_bulk\",\n      \"supported\": true\n    }\n  ],\n  \"command\": \"create\",\n  \"config_seeded\": [\n    \"_config/rnaseq_bulk.yaml\",\n    \"_config/nextflow.slurm.config\"\n  ],\n  \"created\": [\n    \"rnaseq_bulk\"\n  ],\n  \"ok\": true,\n  \"project\": \"/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization\",\n  \"sanitized_title\": \"Macrophage_Polarization\",\n  \"supported_assays\": [\n    {\n      \"assay\": \"ATAC-seq (bulk)\",\n      \"assay_id\": \"atacseq_bulk\"\n    },\n    {\n      \"assay\": \"ChIP-seq (bulk)\",\n      \"assay_id\": \"chipseq_bulk\"\n    },\n    {\n      \"assay\": \"CUT&RUN / CUT&Tag\",\n      \"assay_id\": \"cutandrun\"\n    },\n    {\n      \"assay\": \"Bisulfite (WGBS/RRBS)\",\n      \"assay_id\": \"methylseq\"\n    },\n    {\n      \"assay\": \"Bulk RNA-seq\",\n      \"assay_id\": \"rnaseq_bulk\"\n    }\n  ],\n  \"template_version\": \"v0.9.2\",\n  \"title\": \"Macrophage Polarization\"\n}\n", "stdout_json": {"assays": [{"assay_id": "rnaseq_bulk", "requested": "rnaseq_bulk", "supported": true}], "command": "create", "config_seeded": ["_config/rnaseq_bulk.yaml", "_config/nextflow.slurm.config"], "created": ["rnaseq_bulk"], "ok": true, "project": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization", "sanitized_title": "Macrophage_Polarization", "supported_assays": [{"assay": "ATAC-seq (bulk)", "assay_id": "atacseq_bulk"}, {"assay": "ChIP-seq (bulk)", "assay_id": "chipseq_bulk"}, {"assay": "CUT&RUN / CUT&Tag", "assay_id": "cutandrun"}, {"assay": "Bisulfite (WGBS/RRBS)", "assay_id": "methylseq"}, {"assay": "Bulk RNA-seq", "assay_id": "rnaseq_bulk"}], "template_version": "v0.9.2", "title": "Macrophage Polarization"}, "stderr": "", "stage": "00_initialize_project", "step": "create (Process step 6)"}
{"seq": 10, "t": "2026-08-27T21:54:33-04:00", "type": "snapshot", "label": "after: python3 _system/stage00_register.py create --title", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1289, "content": "# Project: {{project_title}}\n\n| Field | Value |\n|---|---|\n| Created | {{created}} |\n| Template version | {{template_version}} |\n\n## Assays\n\n{{assay_table}}\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n{{source_paths}}\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 490, "content": "# History: {{project_title}}\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## {{created}} — 00_initialize_project — project created\n\nTemplate version: {{template_version}}\nModel: {{model}}\nFile integrity check: `{{integrity}}`\n\n{{source_paths}}\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 11, "t": "2026-08-27T21:54:50-04:00", "type": "agent", "text": "Created: projects/Macrophage_Polarization/\n\n| Assay | Assay ID | Data directory |\n|---|---|---|\n| Bulk RNA-seq | rnaseq_bulk | 00_data/rnaseq_bulk/ |\n\nRaw data path for rnaseq_bulk?", "template": "T3b", "stage": "00_initialize_project", "wait_point": true}
{"seq": 12, "t": "2026-08-27T21:55:01-04:00", "type": "user", "text": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage"}
{"seq": 13, "t": "2026-08-27T21:55:14-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "inspect", "--assay", "rnaseq_bulk", "--source", "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assay_id\": \"rnaseq_bulk\",\n  \"command\": \"inspect\",\n  \"excluded_examples\": [\n    \"notes.txt\"\n  ],\n  \"excluded_file_count\": 1,\n  \"full_check_estimate_min\": 1,\n  \"layout\": \"paired-end\",\n  \"ok\": true,\n  \"raw_file_count\": 8,\n  \"sample_count\": 4,\n  \"sample_ids\": [\n    \"M0_rep1\",\n    \"M0_rep2\",\n    \"M1_rep1\",\n    \"M1_rep2\"\n  ],\n  \"sample_lane_units\": 4,\n  \"source\": \"/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage\",\n  \"total_bytes\": 720,\n  \"total_gb\": 0.0\n}\n", "stdout_json": {"assay_id": "rnaseq_bulk", "command": "inspect", "excluded_examples": ["notes.txt"], "excluded_file_count": 1, "full_check_estimate_min": 1, "layout": "paired-end", "ok": true, "raw_file_count": 8, "sample_count": 4, "sample_ids": ["M0_rep1", "M0_rep2", "M1_rep1", "M1_rep2"], "sample_lane_units": 4, "source": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage", "total_bytes": 720, "total_gb": 0.0}, "stderr": "", "stage": "00_initialize_project", "step": "inspect (Process step 9)"}
{"seq": 14, "t": "2026-08-27T21:55:30-04:00", "type": "agent", "text": "Path: /private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage\nRaw NGS files: 8 (4 R1 / 4 R2, paired-end)\nExcluded (not raw NGS): notes.txt\nSamples: 4\nM0_rep1, M0_rep2, M1_rep1, M1_rep2\n\nConfirm to create symlinks under 00_data/rnaseq_bulk/raw/, or provide a different path.", "template": "T4a", "stage": "00_initialize_project", "wait_point": true}
{"seq": 15, "t": "2026-08-27T21:55:43-04:00", "type": "gate", "gate": "sample_ids", "action": "reached"}
{"seq": 16, "t": "2026-08-27T21:55:43-04:00", "type": "user", "text": "Yes, those are right — go ahead."}
{"seq": 17, "t": "2026-08-27T21:55:44-04:00", "type": "gate", "gate": "sample_ids", "action": "confirmed"}
{"seq": 18, "t": "2026-08-27T21:56:17-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "link", "--project", "projects/Macrophage_Polarization", "--assay", "rnaseq_bulk", "--source", "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assay_id\": \"rnaseq_bulk\",\n  \"broken\": [],\n  \"command\": \"link\",\n  \"linked\": 8,\n  \"ok\": true,\n  \"source\": \"/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage\"\n}\n", "stdout_json": {"assay_id": "rnaseq_bulk", "broken": [], "command": "link", "linked": 8, "ok": true, "source": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage"}, "stderr": "", "stage": "00_initialize_project", "step": "link (Process step 12)"}
{"seq": 19, "t": "2026-08-27T21:56:17-04:00", "type": "snapshot", "label": "after: python3 _system/stage00_register.py link --project", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R2_001.fastq.gz"}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1289, "content": "# Project: {{project_title}}\n\n| Field | Value |\n|---|---|\n| Created | {{created}} |\n| Template version | {{template_version}} |\n\n## Assays\n\n{{assay_table}}\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n{{source_paths}}\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 490, "content": "# History: {{project_title}}\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## {{created}} — 00_initialize_project — project created\n\nTemplate version: {{template_version}}\nModel: {{model}}\nFile integrity check: `{{integrity}}`\n\n{{source_paths}}\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 20, "t": "2026-08-27T21:56:38-04:00", "type": "agent", "text": "Linked 8 files into 00_data/rnaseq_bulk/raw/. Broken links: 0.\nFinalize is running in the background (files.csv, samples.csv, placeholders, exit gate); I will report the result.", "template": "T4b", "stage": "00_initialize_project", "wait_point": false}
{"seq": 21, "t": "2026-08-27T21:56:44-04:00", "type": "command", "argv": ["python3", "_system/stage00_register.py", "finalize", "--project", "projects/Macrophage_Polarization", "--model", "claude-fable-5"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assays\": {\n    \"rnaseq_bulk\": {\n      \"display\": \"Bulk RNA-seq\",\n      \"files\": 8,\n      \"layout\": \"paired-end\",\n      \"samples\": 4,\n      \"samples_csv\": \"created\",\n      \"sources\": [\n        \"/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage\"\n      ],\n      \"units\": 4\n    }\n  },\n  \"command\": \"finalize\",\n  \"created\": \"2026-08-27\",\n  \"failures\": [],\n  \"integrity\": {\n    \"files_checked\": 8,\n    \"mode\": \"quick\"\n  },\n  \"model\": \"claude-fable-5\",\n  \"ok\": true,\n  \"template_version\": \"v0.9.2\"\n}\n", "stdout_json": {"assays": {"rnaseq_bulk": {"display": "Bulk RNA-seq", "files": 8, "layout": "paired-end", "samples": 4, "samples_csv": "created", "sources": ["/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage"], "units": 4}}, "command": "finalize", "created": "2026-08-27", "failures": [], "integrity": {"files_checked": 8, "mode": "quick"}, "model": "claude-fable-5", "ok": true, "template_version": "v0.9.2"}, "stderr": "[integrity] quick check of 8 files, 4 worker(s)\n", "stage": "00_initialize_project", "step": "finalize (Process step 15)"}
{"seq": 22, "t": "2026-08-27T21:56:44-04:00", "type": "snapshot", "label": "after: python3 _system/stage00_register.py finalize --project", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/files.csv", "kind": "file", "mode": "0444", "size": 571, "content": "# generated by stage 00 — do not edit\nsample_id,lane,fastq_1,fastq_2\nM0_rep1,L001,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz\nM0_rep2,L001,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz\nM1_rep1,L001,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz\nM1_rep2,L001,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz\n"}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/samples.csv", "kind": "file", "mode": "0644", "size": 80, "content": "sample_id,condition,group,replicate\nM0_rep1,,,\nM0_rep2,,,\nM1_rep1,,,\nM1_rep2,,,\n"}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1588, "content": "# Project: Macrophage_Polarization\n\n| Field | Value |\n|---|---|\n| Created | 2026-08-27 |\n| Template version | v0.9.2 |\n\n## Assays\n\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n| Bulk RNA-seq | rnaseq_bulk | `00_data/rnaseq_bulk/` | 8 | 4 |\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 660, "content": "# History: Macrophage_Polarization\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## 2026-08-27 — 00_initialize_project — project created\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nFile integrity check: `quick`\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 23, "t": "2026-08-27T21:57:52-04:00", "type": "agent", "text": "Stage 00 complete. Project Macrophage Polarization initialized at projects/Macrophage_Polarization/.\n\n| Assay | Files linked | Samples | Source |\n|---|---|---|---|\n| rnaseq_bulk | 8 | 4 | /private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage |\n\nFile integrity: 8 files checked, mode quick.\n\nWritten: CONTEXT.md, HISTORY.md, and per assay files.csv + samples.csv.\n\nOver to you: fill in the design columns in each 00_data/rnaseq_bulk/samples.csv, one\nrow per sample. To analyse only some samples, delete the other rows — the raw data stays linked,\nso it is reversible.\n\nTell me when the design is filled in and I will validate it and emit the samplesheets.", "template": "T6", "stage": "00_initialize_project", "wait_point": true}
{"seq": 24, "t": "2026-08-27T21:58:16-04:00", "type": "gate", "gate": "design", "action": "reached"}
{"seq": 25, "t": "2026-08-27T21:58:16-04:00", "type": "human_edit", "path": "00_data/rnaseq_bulk/samples.csv", "description": "The human fills the design in an editor: condition (untreated vs LPS_IFNg), group (M0 vs M1), replicate (1,2) — all four rows kept."}
{"seq": 26, "t": "2026-08-27T21:58:16-04:00", "type": "snapshot", "label": "after human edit: 00_data/rnaseq_bulk/samples.csv", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/files.csv", "kind": "file", "mode": "0444", "size": 571, "content": "# generated by stage 00 — do not edit\nsample_id,lane,fastq_1,fastq_2\nM0_rep1,L001,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz\nM0_rep2,L001,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz\nM1_rep1,L001,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz\nM1_rep2,L001,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz\n"}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/samples.csv", "kind": "file", "mode": "0644", "size": 126, "content": "sample_id,condition,group,replicate\nM0_rep1,untreated,M0,1\nM0_rep2,untreated,M0,2\nM1_rep1,LPS_IFNg,M1,1\nM1_rep2,LPS_IFNg,M1,2\n"}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1588, "content": "# Project: Macrophage_Polarization\n\n| Field | Value |\n|---|---|\n| Created | 2026-08-27 |\n| Template version | v0.9.2 |\n\n## Assays\n\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n| Bulk RNA-seq | rnaseq_bulk | `00_data/rnaseq_bulk/` | 8 | 4 |\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 660, "content": "# History: Macrophage_Polarization\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## 2026-08-27 — 00_initialize_project — project created\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nFile integrity check: `quick`\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 27, "t": "2026-08-27T21:58:16-04:00", "type": "gate", "gate": "design", "action": "approved"}
{"seq": 28, "t": "2026-08-27T21:58:16-04:00", "type": "user", "text": "The design is filled in."}
{"seq": 29, "t": "2026-08-27T21:59:14-04:00", "type": "agent", "text": "Starting stage 01: Prepare Samplesheets.\nProject: Macrophage Polarization\nValidating the completed samples.csv for each assay before writing any samplesheet.", "template": "T1", "stage": "01_prepare_samplesheets", "wait_point": false}
{"seq": 30, "t": "2026-08-27T21:59:21-04:00", "type": "command", "argv": ["python3", "_system/stage01_samplesheet.py", "--project", "projects/Macrophage_Polarization", "--check"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assays\": {\n    \"rnaseq_bulk\": {\n      \"config_unfilled\": [\n        \"fasta\",\n        \"gtf\",\n        \"formula\",\n        \"contrast\"\n      ],\n      \"counts\": {\n        \"columns\": [\n          \"sample\",\n          \"fastq_1\",\n          \"fastq_2\",\n          \"strandedness\"\n        ],\n        \"design_rows\": 4,\n        \"full_check_estimate_min\": 1,\n        \"full_check_needs_scheduling\": false,\n        \"groups\": 2,\n        \"included_bytes\": 720,\n        \"included_gb\": 0.0,\n        \"layout\": \"paired-end\",\n        \"samples_included\": 4,\n        \"samples_total\": 4,\n        \"samplesheet_rows\": 4,\n        \"strandedness\": \"auto\"\n      },\n      \"exclusions\": [],\n      \"failures\": [],\n      \"fatal\": false\n    }\n  },\n  \"exclusions_pending\": false,\n  \"existing_outputs\": [],\n  \"mode\": \"check\",\n  \"ok\": true,\n  \"project\": \"projects/Macrophage_Polarization\",\n  \"template_version\": \"v0.9.2\",\n  \"verify_integrity\": \"none\",\n  \"wrote\": []\n}\n", "stdout_json": {"assays": {"rnaseq_bulk": {"config_unfilled": ["fasta", "gtf", "formula", "contrast"], "counts": {"columns": ["sample", "fastq_1", "fastq_2", "strandedness"], "design_rows": 4, "full_check_estimate_min": 1, "full_check_needs_scheduling": false, "groups": 2, "included_bytes": 720, "included_gb": 0.0, "layout": "paired-end", "samples_included": 4, "samples_total": 4, "samplesheet_rows": 4, "strandedness": "auto"}, "exclusions": [], "failures": [], "fatal": false}}, "exclusions_pending": false, "existing_outputs": [], "mode": "check", "ok": true, "project": "projects/Macrophage_Polarization", "template_version": "v0.9.2", "verify_integrity": "none", "wrote": []}, "stderr": "", "stage": "01_prepare_samplesheets", "step": "--check (Process step 3)"}
{"seq": 31, "t": "2026-08-27T21:59:32-04:00", "type": "agent", "text": "Design validated. Before writing the samplesheet:\n\nOptional deep file-integrity check — decompresses each of the 4 included\nsample(s) to catch a truncated or corrupt FASTQ. Stage 00 already confirmed every link resolves\nand is a real gzip; this is the stronger check.\n\n  Data to verify: 0.0 GB\n  Estimated time: ~1 min\n\nMost FASTQs arrive already validated by the sequencing core, so this is off by default.\n\nReply `verify` to run it, or `skip` to trust the files.", "template": "T8", "stage": "01_prepare_samplesheets", "wait_point": true}
{"seq": 32, "t": "2026-08-27T21:59:44-04:00", "type": "gate", "gate": "integrity", "action": "reached"}
{"seq": 33, "t": "2026-08-27T21:59:44-04:00", "type": "user", "text": "verify"}
{"seq": 34, "t": "2026-08-27T21:59:44-04:00", "type": "gate", "gate": "integrity", "action": "confirmed"}
{"seq": 35, "t": "2026-08-27T22:00:14-04:00", "type": "command", "argv": ["python3", "_system/stage01_samplesheet.py", "--project", "projects/Macrophage_Polarization", "--model", "claude-fable-5", "--verify-integrity", "full"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "{\n  \"assays\": {\n    \"rnaseq_bulk\": {\n      \"config_unfilled\": [\n        \"fasta\",\n        \"gtf\",\n        \"formula\",\n        \"contrast\"\n      ],\n      \"counts\": {\n        \"columns\": [\n          \"sample\",\n          \"fastq_1\",\n          \"fastq_2\",\n          \"strandedness\"\n        ],\n        \"design_rows\": 4,\n        \"full_check_estimate_min\": 1,\n        \"full_check_needs_scheduling\": false,\n        \"groups\": 2,\n        \"included_bytes\": 720,\n        \"included_gb\": 0.0,\n        \"layout\": \"paired-end\",\n        \"samples_included\": 4,\n        \"samples_total\": 4,\n        \"samplesheet_rows\": 4,\n        \"strandedness\": \"auto\"\n      },\n      \"exclusions\": [],\n      \"failures\": [],\n      \"fatal\": false\n    }\n  },\n  \"history_entry\": \"## <ISO-8601 date> \\u2014 01_prepare_samplesheets \\u2014 samplesheets emitted\\n\\nTemplate version: v0.9.2\\nModel: claude-fable-5\\nDeep file-integrity verification: `full`\\n\\n- **rnaseq_bulk**: 4 of 4 samples, 2 group(s), paired-end, full_check_estimate_min `1`, full_check_needs_scheduling `False`, included_bytes `720`, included_gb `0.0`, strandedness `auto`. Columns `sample,fastq_1,fastq_2,strandedness`. Wrote 4 samplesheet rows and 4 design rows.\\n\\nFiles written: 01_samplesheets/rnaseq_bulk_samplesheet.csv, 01_samplesheets/rnaseq_bulk_design.csv\",\n  \"mode\": \"write\",\n  \"ok\": true,\n  \"project\": \"projects/Macrophage_Polarization\",\n  \"template_version\": \"v0.9.2\",\n  \"verify_integrity\": \"full\",\n  \"wrote\": [\n    \"01_samplesheets/rnaseq_bulk_samplesheet.csv\",\n    \"01_samplesheets/rnaseq_bulk_design.csv\"\n  ]\n}\n", "stdout_json": {"assays": {"rnaseq_bulk": {"config_unfilled": ["fasta", "gtf", "formula", "contrast"], "counts": {"columns": ["sample", "fastq_1", "fastq_2", "strandedness"], "design_rows": 4, "full_check_estimate_min": 1, "full_check_needs_scheduling": false, "groups": 2, "included_bytes": 720, "included_gb": 0.0, "layout": "paired-end", "samples_included": 4, "samples_total": 4, "samplesheet_rows": 4, "strandedness": "auto"}, "exclusions": [], "failures": [], "fatal": false}}, "history_entry": "## <ISO-8601 date> — 01_prepare_samplesheets — samplesheets emitted\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nDeep file-integrity verification: `full`\n\n- **rnaseq_bulk**: 4 of 4 samples, 2 group(s), paired-end, full_check_estimate_min `1`, full_check_needs_scheduling `False`, included_bytes `720`, included_gb `0.0`, strandedness `auto`. Columns `sample,fastq_1,fastq_2,strandedness`. Wrote 4 samplesheet rows and 4 design rows.\n\nFiles written: 01_samplesheets/rnaseq_bulk_samplesheet.csv, 01_samplesheets/rnaseq_bulk_design.csv", "mode": "write", "ok": true, "project": "projects/Macrophage_Polarization", "template_version": "v0.9.2", "verify_integrity": "full", "wrote": ["01_samplesheets/rnaseq_bulk_samplesheet.csv", "01_samplesheets/rnaseq_bulk_design.csv"]}, "stderr": "[integrity] full check of 8 files, 4 worker(s)\n", "stage": "01_prepare_samplesheets", "step": "write with --verify-integrity full (Process step 9)"}
{"seq": 36, "t": "2026-08-27T22:00:14-04:00", "type": "snapshot", "label": "after: python3 _system/stage01_samplesheet.py --project projects/Macrophage_Polarization", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/files.csv", "kind": "file", "mode": "0444", "size": 571, "content": "# generated by stage 00 — do not edit\nsample_id,lane,fastq_1,fastq_2\nM0_rep1,L001,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz\nM0_rep2,L001,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz\nM1_rep1,L001,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz\nM1_rep2,L001,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz\n"}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/samples.csv", "kind": "file", "mode": "0644", "size": 126, "content": "sample_id,condition,group,replicate\nM0_rep1,untreated,M0,1\nM0_rep2,untreated,M0,2\nM1_rep1,LPS_IFNg,M1,1\nM1_rep2,LPS_IFNg,M1,2\n"}, {"path": "01_samplesheets", "kind": "dir", "mode": "0755", "size": 0}, {"path": "01_samplesheets/rnaseq_bulk_design.csv", "kind": "file", "mode": "0644", "size": 126, "content": "sample_id,condition,group,replicate\nM0_rep1,untreated,M0,1\nM0_rep2,untreated,M0,2\nM1_rep1,LPS_IFNg,M1,1\nM1_rep2,LPS_IFNg,M1,2\n"}, {"path": "01_samplesheets/rnaseq_bulk_samplesheet.csv", "kind": "file", "mode": "0644", "size": 1720, "content": "sample,fastq_1,fastq_2,strandedness\nM0_rep1,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz,auto\nM0_rep2,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz,auto\nM1_rep1,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz,auto\nM1_rep2,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz,auto\n"}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1588, "content": "# Project: Macrophage_Polarization\n\n| Field | Value |\n|---|---|\n| Created | 2026-08-27 |\n| Template version | v0.9.2 |\n\n## Assays\n\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n| Bulk RNA-seq | rnaseq_bulk | `00_data/rnaseq_bulk/` | 8 | 4 |\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 660, "content": "# History: Macrophage_Polarization\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## 2026-08-27 — 00_initialize_project — project created\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nFile integrity check: `quick`\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 37, "t": "2026-08-27T22:00:56-04:00", "type": "agent", "text": "| Assay | Rows | Samples | Groups | Layout | Strandedness |\n|---|---|---|---|---|---|\n| rnaseq_bulk | 4 | 4 of 4 | 2 | paired-end | auto |\n\nAll checks passed. Writing samplesheets.", "template": "T2", "stage": "01_prepare_samplesheets", "wait_point": false}
{"seq": 38, "t": "2026-08-27T22:01:03-04:00", "type": "command", "argv": ["sh", "-c", "cat /private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/history-entry.md >> projects/Macrophage_Polarization/HISTORY.md"], "cwd": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars", "exit_code": 0, "stdout": "", "stdout_json": null, "stderr": "", "stage": "01_prepare_samplesheets", "step": "append history_entry (Process step 13)"}
{"seq": 39, "t": "2026-08-27T22:01:03-04:00", "type": "snapshot", "label": "after: sh -c cat /private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/history-entry.md >> projects/Macrophage_Polarization/HISTORY.md", "root_label": "project", "files": [{"path": "00_data", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "00_data/rnaseq_bulk", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/files.csv", "kind": "file", "mode": "0444", "size": 571, "content": "# generated by stage 00 — do not edit\nsample_id,lane,fastq_1,fastq_2\nM0_rep1,L001,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz\nM0_rep2,L001,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz\nM1_rep1,L001,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz\nM1_rep2,L001,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz\n"}, {"path": "00_data/rnaseq_bulk/raw", "kind": "dir", "mode": "0755", "size": 0}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep1_S3_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M0_rep2_S4_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep1_S1_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R1_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz", "kind": "symlink", "target": "/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage/M1_rep2_S2_L001_R2_001.fastq.gz"}, {"path": "00_data/rnaseq_bulk/samples.csv", "kind": "file", "mode": "0644", "size": 126, "content": "sample_id,condition,group,replicate\nM0_rep1,untreated,M0,1\nM0_rep2,untreated,M0,2\nM1_rep1,LPS_IFNg,M1,1\nM1_rep2,LPS_IFNg,M1,2\n"}, {"path": "01_samplesheets", "kind": "dir", "mode": "0755", "size": 0}, {"path": "01_samplesheets/rnaseq_bulk_design.csv", "kind": "file", "mode": "0644", "size": 126, "content": "sample_id,condition,group,replicate\nM0_rep1,untreated,M0,1\nM0_rep2,untreated,M0,2\nM1_rep1,LPS_IFNg,M1,1\nM1_rep2,LPS_IFNg,M1,2\n"}, {"path": "01_samplesheets/rnaseq_bulk_samplesheet.csv", "kind": "file", "mode": "0644", "size": 1720, "content": "sample,fastq_1,fastq_2,strandedness\nM0_rep1,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep1_S3_L001_R2_001.fastq.gz,auto\nM0_rep2,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M0_rep2_S4_L001_R2_001.fastq.gz,auto\nM1_rep1,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep1_S1_L001_R2_001.fastq.gz,auto\nM1_rep2,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R1_001.fastq.gz,/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/gars-run/gars/projects/Macrophage_Polarization/00_data/rnaseq_bulk/raw/M1_rep2_S2_L001_R2_001.fastq.gz,auto\n"}, {"path": "CONTEXT.md", "kind": "file", "mode": "0644", "size": 1588, "content": "# Project: Macrophage_Polarization\n\n| Field | Value |\n|---|---|\n| Created | 2026-08-27 |\n| Template version | v0.9.2 |\n\n## Assays\n\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n| Bulk RNA-seq | rnaseq_bulk | `00_data/rnaseq_bulk/` | 8 | 4 |\n\n<!-- One row per supported assay:\n| Assay | Assay ID | Data directory | Files | Samples |\n|---|---|---|---|---|\n-->\n\n## Raw data sources\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n\n<!-- One row per assay:\n| Assay ID | Source path | Files linked |\n|---|---|---|\nRaw data is symlinked, never copied. The source path is recorded so a broken link can be traced.\n-->\n\n## Stage state\n\nState is not recorded here. It is derivable from the filesystem:\n\n| Question | Answer from |\n|---|---|\n| Is the design complete? | `00_data/<Assay ID>/samples.csv` — experimental columns filled |\n| Have samplesheets been emitted? | `01_samplesheets/` |\n| How far has an assay run? | `02_bioinformatics/<Assay ID>/<sub-stage>/STATUS` |\n| What did a sub-stage produce? | that sub-stage's `OUTPUTS.tsv` |\n\n`HISTORY.md` records what happened and when. This file records what the project *is*.\n\n## Configuration\n\n`_config/<Assay ID>.yaml` and `_config/nextflow.slurm.config` are written by the user before\nstage 02 runs. Schema: `_references/config_schema.md`. Nothing writes them automatically —\nevery key is a scientific decision the system must not make on the user's behalf.\n"}, {"path": "HISTORY.md", "kind": "file", "mode": "0644", "size": 1196, "content": "# History: Macrophage_Polarization\n\nAppend-only. One dated entry per stage action, newest last. Every stage appends here; no stage\nrewrites or removes an earlier entry.\n\nEntry format:\n\n```\n## <ISO-8601 date> — <stage or sub-stage> — <outcome>\n<what was done, what was written, and where any input came from>\n```\n\n---\n\n## 2026-08-27 — 00_initialize_project — project created\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nFile integrity check: `quick`\n\n| Assay ID | Source path | Files linked |\n|---|---|---|\n| rnaseq_bulk | `/private/tmp/claude-912030806/-Users-<user>-glitch/66f40110-56d7-432f-bfc0-0e0da70c3ef2/scratchpad/seqrun-macrophage` | 8 |\n\n## 2026-08-27 — 01_prepare_samplesheets — samplesheets emitted\n\nTemplate version: v0.9.2\nModel: claude-fable-5\nDeep file-integrity verification: `full`\n\n- **rnaseq_bulk**: 4 of 4 samples, 2 group(s), paired-end, full_check_estimate_min `1`, full_check_needs_scheduling `False`, included_bytes `720`, included_gb `0.0`, strandedness `auto`. Columns `sample,fastq_1,fastq_2,strandedness`. Wrote 4 samplesheet rows and 4 design rows.\n\nFiles written: 01_samplesheets/rnaseq_bulk_samplesheet.csv, 01_samplesheets/rnaseq_bulk_design.csv\n"}, {"path": "_config", "kind": "dir", "mode": "0755", "size": 0}, {"path": "_config/.gitkeep", "kind": "file", "mode": "0644", "size": 0, "content": ""}, {"path": "_config/nextflow.slurm.config", "kind": "file", "mode": "0644", "size": 877, "content": "// Executor settings, passed to the wrapper via --nextflow-config.\n//\n// Required, not optional: Nextflow detects Slurm and submits each pipeline process as its own\n// child job. The partition chosen for the parent job does not apply to them, so without an\n// explicit queue they land wherever Nextflow defaults -- in our case the most contended\n// partition on the cluster.\n//\n// Must define no `params` in any form; the wrapper rejects such configs so its audited\n// parameter surface cannot be bypassed. Executor and process settings are the permitted use.\n\nprocess {\n    executor = 'slurm'\n    queue    = 'cpu_long'\n\n    // 130..145 covers the SIGTERM/SIGKILL family; 104 is a common transient.\n    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }\n    maxRetries    = 3\n}\n\nexecutor {\n    queueSize       = 20\n    submitRateLimit = '10/1min'\n}\n"}, {"path": "_config/rnaseq_bulk.yaml", "kind": "file", "mode": "0644", "size": 3774, "content": "# Configuration for assay rnaseq_bulk, project Macrophage_Polarization\n#\n# Stage 00 put this here so you never author a config from a blank file. Everything that can be\n# filled in for you already has been. What remains is marked <REQUIRED> -- those are scientific\n# decisions, and no stage will substitute a value for them, because a wrong one produces a\n# confident wrong answer rather than an error.\n#\n# Full rationale for every key: _references/config_schema.md\n\n# --- what the reads are ------------------------------------------------------------------------\n# auto | forward | reverse | unstranded\n# `auto` delegates to nf-core's RSeQC check, which cannot return a confident *stranded* call on an\n# unstranded library and reports it as \"N/N samples failed strandedness check\" -- a warning that\n# reads like a failure and is not one. Set it explicitly if the library prep is known.\n# This lab's measured answer (decision 0032): the TALL leukemia libraries are UNSTRANDED --\n# RSeQC sense ~= antisense on 10/10 samples, corroborated by the lab's sns run. For those\n# libraries set `unstranded` explicitly and the warning disappears.\nstrandedness: auto\n\n# --- what to align against ---------------------------------------------------------------------\n# Declare EITHER `genome` OR `fasta` + `gtf`, never both.\n#\n# Do NOT use `genome: GRCh38`. That resolves to the NCBI iGenomes build, which carries no\n# `gene_biotype` attribute, and the run fails at SUBREAD_FEATURECOUNTS *after* counts are written.\n# It cost a full pipeline run once (decision 0005, failure 5). Use the Ensembl FASTA + GTF.\nreference:\n  # You do not need to fill these by hand: stage 02 offers the registered genomes as a menu and\n  # sets fasta, gtf and derived_dir together, so they can never be mismatched. Paste paths here\n  # only if you are using a reference that is not in _references/genomes.md.\n  fasta: <REQUIRED: choose a genome at stage 02, or paste a FASTA path>\n  gtf:   <REQUIRED: choose a genome at stage 02, or paste the matching GTF path>\n\n  # Optional but strongly recommended: a cache of built STAR/Salmon indices, keyed by PIPELINE\n  # version. Without it every run rebuilds ~43 GB of indices, about 40 minutes. A STAR index is\n  # rejected by a different STAR version, which is why the version is part of the path.\n  # derived_dir: ~/install/refs/ensembl-GRCh38-116/derived/nf-core-rnaseq-3.26.0\n\naligner: star_salmon          # star_salmon | star_rsem | hisat2 | bowtie2_salmon\n\n# --- where it runs -----------------------------------------------------------------------------\n# Infrastructure, not science. These are the values verified on this cluster; change them if your\n# allocation differs.\ncompute:\n  partition: cpu_long\n  time: \"5-00:00:00\"\n  cpus: 8\n  mem: 64G\n  # Nextflow's scratch. NEVER inside the project: a single 10-sample run accumulates 250-350 GB\n  # here, because work/ retains every process output so -resume can reuse it. results/ is\n  # published with mode 'copy', so work/ is disposable once a run succeeds.\n  work_dir: <scratch>/gars-work/Macrophage_Polarization\n\n# --- what question the differential expression asks --------------------------------------------\n# Read by sub-stage 02.02. Every formula term must be a column of the design table\n# (01_samplesheets/rnaseq_bulk_design.csv), and both contrast levels must appear in that column.\nde:\n  # Also offered as choices at stage 02: the contrast menu lists the levels your design table\n  # actually contains, in both directions, and refuses one whose level has fewer than 2 samples.\n  formula:  <REQUIRED: defaults to \"~ condition\"; use \"~ batch + condition\" to control for batch>\n  contrast: <REQUIRED: choose at stage 02, or write factor,numerator,denominator e.g. \"condition,MT,WT\">\n"}]}
{"seq": 40, "t": "2026-08-27T22:01:20-04:00", "type": "agent", "text": "Stage 01 complete. Samplesheets written to projects/Macrophage_Polarization/01_samplesheets/.\n\n| Assay | Samplesheet rows | Design rows | Files |\n|---|---|---|---|\n| rnaseq_bulk | 4 | 4 | rnaseq_bulk_samplesheet.csv, rnaseq_bulk_design.csv |\n\nBefore stage 02 runs, 4 decisions remain in _config/rnaseq_bulk.yaml: fasta, gtf, formula,\ncontrast. Nothing is guessed — a wrong reference or contrast produces a confident wrong answer\nrather than an error.\n\nYou do not have to look them up. When you start stage 02 I will offer the registered reference\ngenomes, and the contrasts your design table actually supports, as numbered choices — and show\nyou the finished file before anything runs.\n\nSay when you are ready and I will start the bioinformatics for rnaseq_bulk.", "template": "T4", "stage": "01_prepare_samplesheets", "wait_point": true}
{"seq": 41, "t": "2026-08-27T22:01:45-04:00", "type": "end", "outcome": "complete", "summary": "Full stage 00 -> 01 walk: 8 FASTQs registered (decoy excluded), sample IDs confirmed at the gate, design filled by the human, deep integrity verified, samplesheets written. Stage 02 pipeline config continues in the precomputed scenarios."}